Microbiological growth in cooling systems water may result in biofilm formation, which can cause problems of bio-corrosion, pressure drop in the pipes, reduction of heat transfer rate and flow obstruction. The main and traditional biocides applied in microbiological control of cooling waters are the chlorine based compounds. However, in recent years, peracetic acid has become an alternative to chlorinated compounds, since this biocide leaves as residue only the acetate, which is biodegradable and does not form chlorinated organic byproducts. This work analyzed the application of peracetic acid comparing to sodium hypochlorite in the microbiological control and material corrosivity using a laboratory scale test tree. The corrosion rate of carbon steel, copper and stainless steel alloys in addition to the effectiveness in reducing the bacterial count. The experiments were carried out under conditions of turbulent flow, pH 8 and temperature of 32 C using a real industrial test water loaded with organics (COD = 350 mg/L). Peracetic acid concentrations used were 0.75, 1.0 and 3.0 mg/L and sodium hypochlorite were 1.0 and 3.0 mg/L. Peracetic acid at the concentration of 3.0 mg/L decreased the bacterial load from 1.5x10 (raised to 5) UFC/mL to 5.24x10 (raised to 3) UFC/mL. Peracetic acid compared to sodium hypochlorite was less corrosive to carbon steel at all concentrations. At the concentration of 1.0 mg/L the corrosion rate of copper in peracetic acid was lower than in sodium hypochlorite solution. At the concentration of 3.0 mg/L, the reverse occurred. No significant corrosion was observed in stainless steel for the biocides studied.